Variant report

Variant	rs2705544
Chromosome Location	chr3:112186751-112186752
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs12632867	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1386895	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1398091	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1512006	0.82[CEU][hapmap]
rs1533159	0.86[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs1814052	0.93[EUR][1000 genomes]
rs1844089	0.81[CHB][hapmap]
rs1873571	0.81[CHB][hapmap]
rs1873572	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs1877363	0.82[CEU][hapmap]
rs2171513	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2171514	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2633556	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2633557	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2633560	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2633562	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2633563	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2633574	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2633578	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2633579	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes]
rs2633580	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2633582	0.81[CHB][hapmap]
rs2633588	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2633589	0.93[EUR][1000 genomes]
rs2638013	0.93[EUR][1000 genomes]
rs2638015	0.89[EUR][1000 genomes]
rs2638016	0.81[CHB][hapmap]
rs2638017	0.81[CHB][hapmap]
rs2638019	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2638022	0.81[CHB][hapmap]
rs2638023	0.86[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap]
rs2638026	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2638029	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2638031	0.81[CHB][hapmap]
rs2638032	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2638035	0.86[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap]
rs2638037	0.81[CHB][hapmap]
rs2638039	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs2705507	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2705521	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2705522	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2705525	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2705533	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2705534	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2705535	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2705536	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2705541	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2705555	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2705556	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2705559	0.81[CHB][hapmap]
rs2705562	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2705565	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.93[EUR][1000 genomes]
rs2705566	0.85[CHB][hapmap]
rs2933134	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2933135	0.86[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs2952319	0.86[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs2952323	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2952325	0.90[JPT][hapmap]
rs2952326	0.81[CHB][hapmap]
rs2952327	0.81[CHB][hapmap]
rs2969895	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2969896	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2971204	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2971205	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4519670	0.83[EUR][1000 genomes]
rs4682410	0.82[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs6438079	1.00[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs6792947	0.82[CEU][hapmap]
rs728568	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs7652377	0.82[CEU][hapmap]
rs766968	0.82[CEU][hapmap]
rs9288952	0.82[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs9848054	0.82[CEU][hapmap]
rs9866734	0.82[CEU][hapmap]
rs9869455	1.00[CEU][hapmap]
rs9869579	1.00[CEU][hapmap];0.80[CHB][hapmap]
rs998036	0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2705544	SLC35A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112179800-112189800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112180400-112195400	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr3:112182200-112193600	Weak transcription	Spleen	Spleen
4	chr3:112183800-112186800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:112183800-112188600	Weak transcription	HSMM	muscle
6	chr3:112183800-112195000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:112184000-112186800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:112184200-112188000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:112184200-112190600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:112184200-112191600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:112184600-112187200	Genic enhancers	Primary T cells from cord blood	blood
12	chr3:112185000-112190600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:112185000-112190600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:112185200-112188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:112185200-112190200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:112185200-112190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:112185400-112190200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:112185400-112190400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:112185400-112192200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:112186000-112186800	Strong transcription	Primary B cells from cord blood	blood
21	chr3:112186000-112194400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr3:112186200-112187000	Enhancers	HSMMtube	muscle
23	chr3:112186200-112187200	Enhancers	Primary hematopoietic stem cells	blood
24	chr3:112186200-112189000	ZNF genes & repeats	GM12878-XiMat	blood
25	chr3:112186400-112186800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:112186400-112187000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:112186400-112187000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:112186400-112187000	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr3:112186400-112187000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:112186400-112187000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:112186400-112187000	Enhancers	Fetal Thymus	thymus
32	chr3:112186400-112187000	Enhancers	Thymus	Thymus
33	chr3:112186400-112187200	Enhancers	Adipose Nuclei	Adipose
34	chr3:112186400-112188600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:112186400-112192000	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:112186400-112194400	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr3:112186400-112195000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:112186400-112195200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr3:112186400-112195200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:112186600-112186800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr3:112186600-112186800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:112186600-112187400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:112186600-112188600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:112186600-112188800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr3:112186600-112189200	Weak transcription	Aorta	Aorta

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